data_6KDY # _model_server_result.job_id QIQKZuov5WpFx9ajp4Iu3w _model_server_result.datetime_utc '2024-12-21 12:19:26' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6kdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 6KDY # _exptl.entry_id 6KDY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.31 _cell.angle_gamma 90 _cell.entry_id 6KDY _cell.length_a 99.46 _cell.length_b 162.979 _cell.length_c 114.407 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KDY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J 1 1 C,D,K,L,M 2 1 E,F,N,O 3 1 G,H,P,Q 4 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 K N N ? 3 N N N ? 3 P N N # _chem_comp.formula 'C21 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PA O1A NAD doub 300 n n PA O2A NAD sing 301 n n PA O5B NAD sing 302 n n PA O3 NAD sing 303 n n O2A HOA2 NAD sing 304 n n O5B C5B NAD sing 305 n n C5B C4B NAD sing 306 n n C5B H51A NAD sing 307 n n C5B H52A NAD sing 308 n n C4B O4B NAD sing 309 n n C4B C3B NAD sing 310 n n C4B H4B NAD sing 311 n n O4B C1B NAD sing 312 n n C3B O3B NAD sing 313 n n C3B C2B NAD sing 314 n n C3B H3B NAD sing 315 n n O3B HO3A NAD sing 316 n n C2B O2B NAD sing 317 n n C2B C1B NAD sing 318 n n C2B H2B NAD sing 319 n n O2B HO2A NAD sing 320 n n C1B N9A NAD sing 321 n n C1B H1B NAD sing 322 n n N9A C8A NAD sing 323 n y N9A C4A NAD sing 324 n y C8A N7A NAD doub 325 n y C8A H8A NAD sing 326 n n N7A C5A NAD sing 327 n y C5A C6A NAD sing 328 n y C5A C4A NAD doub 329 n y C6A N6A NAD sing 330 n n C6A N1A NAD doub 331 n y N6A H61A NAD sing 332 n n N6A H62A NAD sing 333 n n N1A C2A NAD sing 334 n y C2A N3A NAD doub 335 n y C2A H2A NAD sing 336 n n N3A C4A NAD sing 337 n y O3 PN NAD sing 338 n n PN O1N NAD doub 339 n n PN O2N NAD sing 340 n n PN O5D NAD sing 341 n n O5D C5D NAD sing 342 n n C5D C4D NAD sing 343 n n C5D H51N NAD sing 344 n n C5D H52N NAD sing 345 n n C4D O4D NAD sing 346 n n C4D C3D NAD sing 347 n n C4D H4D NAD sing 348 n n O4D C1D NAD sing 349 n n C3D O3D NAD sing 350 n n C3D C2D NAD sing 351 n n C3D H3D NAD sing 352 n n O3D HO3N NAD sing 353 n n C2D O2D NAD sing 354 n n C2D C1D NAD sing 355 n n C2D H2D NAD sing 356 n n O2D HO2N NAD sing 357 n n C1D N1N NAD sing 358 n n C1D H1D NAD sing 359 n n N1N C2N NAD sing 360 n y N1N C6N NAD doub 361 n y C2N C3N NAD doub 362 n y C2N H2N NAD sing 363 n n C3N C7N NAD sing 364 n n C3N C4N NAD sing 365 n y C7N O7N NAD doub 366 n n C7N N7N NAD sing 367 n n N7N H71N NAD sing 368 n n N7N H72N NAD sing 369 n n C4N C5N NAD doub 370 n y C4N H4N NAD sing 371 n n C5N C6N NAD sing 372 n y C5N H5N NAD sing 373 n n C6N H6N NAD sing 374 n n # _atom_sites.entry_id 6KDY _atom_sites.fract_transf_matrix[1][1] 0.010054 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001828 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006136 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008884 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code I 3 NAD A 1 401 3 NAD NAD . J 4 PG4 B 1 401 2 PG4 PG4 . K 3 NAD C 1 401 2 NAD NAD . L 5 2PE D 1 401 1 2PE 2PE . M 4 PG4 D 1 402 1 PG4 PG4 . N 3 NAD E 1 401 1 NAD NAD . O 6 PE7 F 1 401 1 PE7 PE7 . P 3 NAD G 1 401 4 NAD NAD . Q 7 P6G H 1 401 1 P6G P6G . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PA NAD . . . N 3 77.778 -44.09 40.478 1 92.94 ? PA NAD 401 E 1 HETATM 2 O O1A NAD . . . N 3 77.245 -43.1 39.481 1 86.02 ? O1A NAD 401 E 1 HETATM 3 O O2A NAD . . . N 3 78.92 -43.501 41.25 1 90.41 ? O2A NAD 401 E 1 HETATM 4 O O5B NAD . . . N 3 78.247 -45.453 39.676 1 86.11 ? O5B NAD 401 E 1 HETATM 5 C C5B NAD . . . N 3 77.268 -46.458 39.766 1 82.95 ? C5B NAD 401 E 1 HETATM 6 C C4B NAD . . . N 3 77.735 -47.741 38.998 1 86.35 ? C4B NAD 401 E 1 HETATM 7 O O4B NAD . . . N 3 78.775 -47.492 38.2 1 86.51 ? O4B NAD 401 E 1 HETATM 8 C C3B NAD . . . N 3 78.223 -48.683 40.09 1 94.9 ? C3B NAD 401 E 1 HETATM 9 O O3B NAD . . . N 3 78.027 -49.978 39.644 1 96.82 ? O3B NAD 401 E 1 HETATM 10 C C2B NAD . . . N 3 79.729 -48.301 40.191 1 92.13 ? C2B NAD 401 E 1 HETATM 11 O O2B NAD . . . N 3 80.554 -49.381 40.83 1 92.98 ? O2B NAD 401 E 1 HETATM 12 C C1B NAD . . . N 3 80.073 -48.089 38.97 1 88.48 ? C1B NAD 401 E 1 HETATM 13 N N9A NAD . . . N 3 81.203 -47.159 38.726 1 84.97 ? N9A NAD 401 E 1 HETATM 14 C C8A NAD . . . N 3 81.142 -45.833 38.842 1 80.53 ? C8A NAD 401 E 1 HETATM 15 N N7A NAD . . . N 3 82.32 -45.297 38.59 1 74.26 ? N7A NAD 401 E 1 HETATM 16 C C5A NAD . . . N 3 83.155 -46.315 38.284 1 82.67 ? C5A NAD 401 E 1 HETATM 17 C C6A NAD . . . N 3 84.492 -46.387 37.931 1 87 ? C6A NAD 401 E 1 HETATM 18 N N6A NAD . . . N 3 85.384 -45.274 37.802 1 92.48 ? N6A NAD 401 E 1 HETATM 19 N N1A NAD . . . N 3 85.074 -47.558 37.671 1 85.67 ? N1A NAD 401 E 1 HETATM 20 C C2A NAD . . . N 3 84.332 -48.705 37.76 1 85.84 ? C2A NAD 401 E 1 HETATM 21 N N3A NAD . . . N 3 83.047 -48.66 38.095 1 84.77 ? N3A NAD 401 E 1 HETATM 22 C C4A NAD . . . N 3 82.447 -47.488 38.357 1 84.78 ? C4A NAD 401 E 1 HETATM 23 O O3 NAD . . . N 3 76.659 -44.654 41.538 1 99.3 ? O3 NAD 401 E 1 HETATM 24 P PN NAD . . . N 3 75.445 -43.9 42.332 1 89.48 ? PN NAD 401 E 1 HETATM 25 O O1N NAD . . . N 3 74.936 -44.785 43.44 1 83.84 ? O1N NAD 401 E 1 HETATM 26 O O2N NAD . . . N 3 74.335 -43.634 41.355 1 86.16 ? O2N NAD 401 E 1 HETATM 27 O O5D NAD . . . N 3 75.957 -42.476 42.953 1 93.13 ? O5D NAD 401 E 1 HETATM 28 C C5D NAD . . . N 3 76.604 -42.433 44.196 1 91.46 ? C5D NAD 401 E 1 HETATM 29 C C4D NAD . . . N 3 76.907 -41.046 44.582 1 87.56 ? C4D NAD 401 E 1 HETATM 30 O O4D NAD . . . N 3 77.725 -40.484 43.689 1 90.06 ? O4D NAD 401 E 1 HETATM 31 C C3D NAD . . . N 3 75.531 -40.148 44.648 1 84.51 ? C3D NAD 401 E 1 HETATM 32 O O3D NAD . . . N 3 75.302 -39.699 46.023 1 84.3 ? O3D NAD 401 E 1 HETATM 33 C C2D NAD . . . N 3 75.666 -39.213 43.795 1 82.74 ? C2D NAD 401 E 1 HETATM 34 O O2D NAD . . . N 3 75.048 -37.92 44.269 1 89.56 ? O2D NAD 401 E 1 HETATM 35 C C1D NAD . . . N 3 77.222 -39.095 43.536 1 85.64 ? C1D NAD 401 E 1 HETATM 36 N N1N NAD . . . N 3 77.476 -38.649 42.325 1 91.26 ? N1N NAD 401 E 1 HETATM 37 C C2N NAD . . . N 3 78.443 -37.639 42.242 1 91.75 ? C2N NAD 401 E 1 HETATM 38 C C3N NAD . . . N 3 78.756 -37.105 40.965 1 91.02 ? C3N NAD 401 E 1 HETATM 39 C C7N NAD . . . N 3 79.842 -36.026 40.641 1 91.23 ? C7N NAD 401 E 1 HETATM 40 O O7N NAD . . . N 3 80.89 -36.188 40.015 1 94.39 ? O7N NAD 401 E 1 HETATM 41 N N7N NAD . . . N 3 79.784 -34.785 41.389 1 89.83 ? N7N NAD 401 E 1 HETATM 42 C C4N NAD . . . N 3 78.093 -37.589 39.913 1 85.63 ? C4N NAD 401 E 1 HETATM 43 C C5N NAD . . . N 3 77.175 -38.579 40.009 1 85.03 ? C5N NAD 401 E 1 HETATM 44 C C6N NAD . . . N 3 76.822 -39.105 41.196 1 91.97 ? C6N NAD 401 E 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #